Our present study provides several lines of evidence showing that TAK1 activation plays an important role in Shh pathway inhibition-induced autophagy in thyroid tumor cell lines: (1) The inhibitors of Gli1 and Smo as well as Gli1 siRNA induced TAK1 phosphorylation, LC3 lipidation, and the formation of autophagosomes; (2) Gli1 overexpression decreased the basal levels of LC3 lipidation; (3) TAK1 inhibition by 5Z and by siRNA blocked GANT61-induced autophagy and phosphorylation of AMPK and JNK. Here, GLI1 is linked to thyroid tumor.